├── .Rbuildignore ├── .github ├── .gitignore └── workflows │ ├── R-CMD-check.yaml │ ├── pkgdown.yaml │ └── test-coverage.yaml ├── .gitignore ├── DESCRIPTION ├── LICENSE.md ├── NAMESPACE ├── R ├── RcppExports.R ├── SCP-analysis.R ├── SCP-app.R ├── SCP-cell_annotation.R ├── SCP-cellqc.R ├── SCP-feature_annotation.R ├── SCP-imputation.R ├── SCP-plot.R ├── SCP-projection.R ├── SCP-workflow.R ├── Seurat-function.R ├── data.R ├── ggsankey.R ├── reexports.R ├── utils.R └── zzz.R ├── README.Rmd ├── README.md ├── SCP.Rproj ├── _pkgdown.yml ├── data ├── ifnb_sub.rda ├── lifemap_cell.rda ├── lifemap_compartment.rda ├── lifemap_organ.rda ├── palette_list.rda ├── panc8_sub.rda ├── pancreas_sub.rda ├── ref_scHCL.rda ├── ref_scMCA.rda ├── ref_scZCL.rda └── words_excluded.rda ├── inst └── python │ ├── SCP_analysis.py │ ├── __pycache__ │ ├── SCP_analysis.cpython-36.pyc │ ├── SCP_analysis.cpython-37.pyc │ └── SCP_analysis.cpython-38.pyc │ └── harmonizomeapi.py ├── man ├── AnnotateFeatures.Rd ├── BBKNN_integrate.Rd ├── CC_GenePrefetch.Rd ├── CSS_integrate.Rd ├── CellCorHeatmap.Rd ├── CellDensityPlot.Rd ├── CellDimPlot.Rd ├── CellDimPlot3D.Rd ├── CellScoring.Rd ├── CellStatPlot.Rd ├── ComBat_integrate.Rd ├── Conos_integrate.Rd ├── CreateDataFile.Rd ├── CreateMetaFile.Rd ├── DefaultReduction.Rd ├── DynamicHeatmap.Rd ├── DynamicPlot.Rd ├── EnrichmentPlot.Rd ├── Env_requirements.Rd ├── FeatureCorPlot.Rd ├── FeatureDimPlot.Rd ├── FeatureDimPlot3D.Rd ├── FeatureHeatmap.Rd ├── FeatureStatPlot.Rd ├── FetchH5.Rd ├── GSEAPlot.Rd ├── GeneConvert.Rd ├── GraphPlot.Rd ├── GroupHeatmap.Rd ├── Harmony_integrate.Rd ├── Integration_SCP.Rd ├── LIGER_integrate.Rd ├── LineagePlot.Rd ├── ListDB.Rd ├── MNN_integrate.Rd ├── PAGAPlot.Rd ├── PrepareDB.Rd ├── PrepareEnv.Rd ├── PrepareSCExplorer.Rd ├── ProjectionPlot.Rd ├── RecoverCounts.Rd ├── RenameClusters.Rd ├── RenameFeatures.Rd ├── RunCSSMap.Rd ├── RunCellQC.Rd ├── RunDEtest.Rd ├── RunDM.Rd ├── RunDimReduction.Rd ├── RunDoubletCalling.Rd ├── RunDynamicEnrichment.Rd ├── RunDynamicFeatures.Rd ├── RunEnrichment.Rd ├── RunFR.Rd ├── RunGLMPCA.Rd ├── RunGSEA.Rd ├── RunHarmony2.Rd ├── RunKNNMap.Rd ├── RunKNNPredict.Rd ├── RunLargeVis.Rd ├── RunMDS.Rd ├── RunMonocle2.Rd ├── RunMonocle3.Rd ├── RunNMF.Rd ├── RunPAGA.Rd ├── RunPCAMap.Rd ├── RunPHATE.Rd ├── RunPaCMAP.Rd ├── RunPalantir.Rd ├── RunSCExplorer.Rd ├── RunSCVELO.Rd ├── RunScmap.Rd ├── RunSeuratMap.Rd ├── RunSingleR.Rd ├── RunSlingshot.Rd ├── RunSymphonyMap.Rd ├── RunTriMap.Rd ├── RunUMAP2.Rd ├── RunWOT.Rd ├── Scanorama_integrate.Rd ├── Seurat_integrate.Rd ├── SrtAppend.Rd ├── SrtReorder.Rd ├── Standard_SCP.Rd ├── StatPlot.Rd ├── Uncorrected_integrate.Rd ├── VelocityPlot.Rd ├── VolcanoPlot.Rd ├── adata_to_srt.Rd ├── adjcolors.Rd ├── as_matrix.Rd ├── blendcolors.Rd ├── capitalize.Rd ├── check_DataType.Rd ├── check_Python.Rd ├── check_R.Rd ├── check_srtList.Rd ├── check_srtMerge.Rd ├── compute_velocity_on_grid.Rd ├── conda_install.Rd ├── conda_python.Rd ├── db_DoubletDetection.Rd ├── db_Scrublet.Rd ├── db_scDblFinder.Rd ├── db_scds.Rd ├── download.Rd ├── drop_data.Rd ├── env_exist.Rd ├── exist_Python_pkgs.Rd ├── fastMNN_integrate.Rd ├── figures │ ├── CellDimPlot3D-1.png │ ├── DynamicHeatmap-1.png │ ├── DynamicPlot-1.png │ ├── EDA-1.png │ ├── EDA-2.png │ ├── EDA-3.png │ ├── EDA-4.png │ ├── EDA-5.png │ ├── Enrichment_comparison-1.png │ ├── Enrichment_enrichmap-1.png │ ├── Example-1.jpg │ ├── Example-2.jpg │ ├── Example-3.jpg │ ├── Example-4.jpg │ ├── FeatureDimPlot3D-1.png │ ├── FeatureHeatmap-1.png │ ├── FeatureStatPlot-1.png │ ├── GSEA_bar-1.png │ ├── GSEA_comparison-1.png │ ├── Integration-all.png │ ├── Integration_SCP-1.png │ ├── RunCellQC-1.png │ ├── RunCellQC-2.png │ ├── RunCellQC-3.png │ ├── RunDEtest-1.png │ ├── RunEnrichment-1.png │ ├── RunEnrichment-2.png │ ├── RunEnrichment-3.png │ ├── RunEnrichment-4.png │ ├── RunGSEA-1.png │ ├── RunKNNMap-1.png │ ├── RunKNNPredict-bulk-1.png │ ├── RunKNNPredict-scrna-1.png │ ├── RunKNNPredict-scrna-2.png │ ├── RunKNNPredict-scrna-3.png │ ├── RunPAGA-1.png │ ├── RunSCVELO-1.png │ ├── RunSCVELO-2.png │ ├── RunSlingshot-1.png │ ├── RunSlingshot-2.png │ ├── RunSlingshot-3.png │ ├── SCExplorer-1.png │ ├── SCExplorer-2.png │ └── Standard_SCP-1.png ├── find_conda.Rd ├── geom_alluvial.Rd ├── geom_alluvial_label.Rd ├── geom_sankey.Rd ├── geom_sankey_bump.Rd ├── geom_sankey_label.Rd ├── get_vars.Rd ├── ifnb_sub.Rd ├── installed_Python_pkgs.Rd ├── invoke.Rd ├── isOutlier.Rd ├── iterchunks.Rd ├── lifemap_cell.Rd ├── make_long.Rd ├── palette_list.Rd ├── palette_scp.Rd ├── panc8_sub.Rd ├── pancreas_sub.Rd ├── panel_fix.Rd ├── reexports.Rd ├── ref_scHCL.Rd ├── scVI_integrate.Rd ├── segementsDf.Rd ├── show_palettes.Rd ├── slim_data.Rd ├── srt_to_adata.Rd ├── theme_blank.Rd ├── theme_sankey.Rd ├── theme_scp.Rd ├── tochunks.Rd ├── try_get.Rd ├── unnest.Rd └── words_excluded.Rd └── src ├── RcppExports.cpp └── asMatrix.cpp /.Rbuildignore: 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